X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=alignmentdb.cpp;h=6909f47b1235c72b67ae409907af97346dfa8007;hb=fee6c80b2ca01d5efd0da8a70bdf07475b23e9da;hp=e2b1dc197eb8d3399156a3ca752bff5da267101f;hpb=260ae19c36cb11a53ddc5a75b5e507f8dd8b31d6;p=mothur.git

diff --git a/alignmentdb.cpp b/alignmentdb.cpp
index e2b1dc1..6909f47 100644
--- a/alignmentdb.cpp
+++ b/alignmentdb.cpp
@@ -74,7 +74,7 @@ AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gap
 				if (temp.getName() != "") {
 					templateSequences.push_back(temp);
 					//save longest base
-					if (temp.getUnaligned().length() > longest)  { longest = temp.getUnaligned().length()+1; }
+					if (temp.getUnaligned().length() >= longest)  { longest = temp.getUnaligned().length()+1; }
 				}
 			}
 			
@@ -94,11 +94,10 @@ AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gap
 			if (temp.getName() != "") {
 				templateSequences.push_back(temp);
 				//save longest base
-				if (temp.getUnaligned().length() > longest)  { longest = temp.getUnaligned().length()+1; }
+				if (temp.getUnaligned().length() >= longest)  { longest = (temp.getUnaligned().length()+1); }
 			}
 		}
 		fastaFile.close();
-		
 	#endif
 	
 		numSeqs = templateSequences.size();
@@ -130,7 +129,7 @@ AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gap
 			#endif
 		}
 		else if(method == "suffix")		{	search = new SuffixDB(numSeqs);								}
-		else if(method == "blast")		{	search = new BlastDB(gapOpen, gapExtend, match, misMatch);	}
+		else if(method == "blast")		{	search = new BlastDB(fastaFileName.substr(0,fastaFileName.find_last_of(".")+1), gapOpen, gapExtend, match, misMatch);	}
 		else {
 			m->mothurOut(method + " is not a valid search option. I will run the command using kmer, ksize=8.");
 			m->mothurOutEndLine();